Climate change, sea level rise, over-pumping and saltwater intrusion present some of the future challenges of water resources management in coastal areas. Over-abstraction is considered one of the main causes of seawater intrusion and the rise in sea levels accelerates the intrusion. With the combined impact of sea level rise and over-pumping the problem becomes exacerbated and requires urgent solutions. Previous studies have mainly focused on the study of impact of sea level rise or over-abstraction on seawater intrusion separately and their combined effects have not been studied in the literature. This paper presents application of a coupled transient density-dependent finite element model to simulate seawater intrusion in coastal aquifers and investigates the individual and combined effects of likely sea level rise and over-pumping on seawater intrusion. Three scenarios are considered: rise in sea levels due to climate change, decline in groundwater table due to over-pumping and combination of sea level rise and over-pumping. The results show that, in the case study considered in this paper, the rise in the sea level moved the transition zone inland by about 5%. However, the combination of sea level rise and over-pumping resulted in further inland movement of the transition zone (about 8%). The amount of intrusion greatly depends on the depth, size and properties of the aquifer. While the intrusion is a few metres in a small aquifer, it could be several kilometres in a large aquifer.